SAM (Significance Analysis of Microarray) Results

Description of the problem:

Number of classes: 2
Number of genes: 12776
Number of genes that passed filtering criteria: 8324
Type of test used: SAM – Significance analysis of Microarray
Column of the Experiment Descriptors sheet that defines class variable : GROUP

Genes which discriminate among classes:

Table 1
There are 166 genes significant by SAM
The median false discovery rate among the 166 significant genes is 0.08539
The delta value used to identify the significant genes is 0.59305
The fudge factor for standard deviation is computed as 0.03459

Geometric mean of ratios
( Disease / Normal )
Qiagen oligo ID Description GB acc UG cluster Gene symbol
1 1.553 H002655_01 Collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive) L02870 1640 COL7A1
2 1.453 H007688_01 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 AF109735 195471 PFKFB3
3 1.757 H002994_01 Collagen, type XVIII, alpha 1 AF018081 78409 COL18A1
4 1.689 H016341_01 Platelet derived growth factor C NM_016205 43080 PDGFC
5 1.422 H006183_01 Metallothionein 1X X65607 278462 MT1X
6 1.251 H011854_01 Heterogeneous nuclear
ribonucleoprotein C (C1/C2)
M16342 182447 HNRPC
7 1.352 H000498_01 Desmoplakin (DPI, DPII) AL031058 74316 DSP
8 1.249 H003776_01 Aldehyde dehydrogenase 2 family
(mitochondrial)
X05409 195432 ALDH2
9 1.436 H012791_01 Metallothionein 1A (functional) K01383 203967 MT1A
10 1.314 H003383_01 Ras-related C3 botulinum toxin
substrate 2 (rho family, small GTP binding protein Rac2)
Z82188 173466 RAC2
11 1.66 H015187_01 Homo sapiens clone N97
immunoglobulin heavy chain variable region mRNA, partial CDS
AF103295 283882
12 1.483 H008423_01 EH-domain containing 3 NM_014600 87125 EHD3
13 1.333 H007009_01 Fibroblast growth factor
receptor-like 1
AK000530 193326 FGFRL1
14 1.23 H000238_01 KRAB associated protein 1 X97548 228059 TIF1B
15 1.386 H011703_01 Hypothetical protein FLJ20364 AK000371 32471 FLJ20364
16 1.292 H014948_01 Phosphatidylglycerophosphate
Synthase
NM_024419 278682 PGS1
17 1.375 H006492_01 Homo sapiens CD44 isoform RC
(CD44) mRNA, complete CDS
AF098641 306278
18 1.374 H012664_01 metallothionein 1B (functional) M13485 211924 MT1B
19 1.292 H006579_01 Hypothetical protein FLJ10292 AK001154 104650 FLJ10292
20 1.427 H008064_01 KIAA0008 gene product D13633 77695 KIAA0008
21 1.255 H012398_01 KIAA1118 protein AB029041 209646 KIAA1118
22 1.451 H003725_01 Cartilage oligomeric matrix
protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)
AC003107 1584 COMP
23 1.211 H011172_01 Heat shock protein 75 NM_016292 182366 TRAP1
24 1.243 H009594_01 Neuropathy target esterase AJ004832 5038 NTE
25 1.445 H008685_01 Metallothionein 2A V00594 118786 MT2A
26 1.279 H007583_01 Kinesin family member 4A AF071592 279766 KIF4A
27 1.367 H013251_01 KIAA1329 protein AB037750 21061 KIAA1329
28 1.189 H015295_01 Homo sapiens HSPC337 mRNA,
partial CDS
AF161451 284295
29 1.5 H011653_01 Vanilloid receptor-like protein NM_016113 300686 VRL
30 1.405 H012717_01 Metallothionein 1F (functional) M10943 203936 MT1F
31 1.193 H003987_01 PRO0659 protein NM_014138 6451 PRO0659
32 1.415 H009923_01 Vanilloid receptor-like protein 1 NM_015930 279746 VRL-1
33 1.313 H016122_01 TMTSP for transmembrane molecule
with thrombospondin module
NM_018676 325667 LOC55901
34 1.244 H012710_01 Hepatitis delta
antigen-interacting protein A
U63825 66713 DIPA
35 0.621 H003528_01 Decay accelerating factor for
complement (CD55, Cromer blood group system)
M30142 1369 DAF
36 0.548 H003827_01 Serum/glucocorticoid regulated
kinase
AJ000512 296323 SGK
37 0.548 H016371_01 Hypothetical protein FLJ21212 NM_024642 47099 FLJ21212
38 0.584 H009347_01 Neuronal cell adhesion molecule AB002341 7912 NRCAM
39 0.465 H001509_01 Aldo-keto reductase family 1,
member C3 (3-alpha hydroxysteroid dehydrogenase, type II)
D17793 78183 AKR1C3
40 0.517 H003858_01 Aldo-keto reductase family 1,
member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-a
U05598 201967 AKR1C2
41 0.62 H010655_01 Hypothetical protein FLJ20546 AK000953 279896 FLJ20546
42 0.811 H005438_01 Homo sapiens mRNA; cDNA DKFZp434B1620 (from clone DKFZp434B1620) AL137548 43112
43 0.728 H004078_01 Heme-binding protein NM_015987 108675 HEBP
44 0.708 H002860_01 Inositol
polyphosphate-1-phosphatase
L08488 32309 INPP1
45 0.768 H002574_01 Alcohol dehydrogenase 5 (class
III), chi polypeptide
M81118 78989 ADH5
46 0.751 H004767_01 Tetraspan 3 AK001326 100090 TSPAN-3
47 0.629 H010640_01 Homo sapiens mRNA; cDNA
DKFZp434B1272 (from clone DKFZp434B1272); partial CDS
AL162032 158258
48 0.689 H000959_01 Glycophorin C (Gerbich blood
group)
NM_002101 81994 GYPC
49 0.721 H003965_01 Cellular repressor of
E1A-stimulated genes
AF084523 5710 CREG
50 0.724 H002462_01 Receptor tyrosine kinase-like
orphan receptor 1
M97675 274243 ROR1
51 0.664 H007733_01 Retinal short-chain
dehydrogenase/reductase retSDR3
NM_016246 18788 LOC51171
52 0.771 H016494_01 Hypothetical protein FLJ12436 NM_024661 69485 FLJ12436
53 0.742 H008089_01 KIAA0469 gene product AB007938 7764 KIAA0469
54 0.631 H007034_01 Histamine N-methyltransferase U44111 81182 HNMT
55 0.706 H000410_01 A kinase (PRKA) anchor protein
(gravin) 12
U81607 788 AKAP12
56 0.702 H001356_01 KIAA0537 gene product AB011109 200598 KIAA0537
57 0.538 H001341_01 Platelet-derived growth factor
receptor-like
D37965 170040 PDGFRL
58 0.815 H002021_01 V-maf musculoaponeurotic
fibrosarcoma (avian) oncogene family, protein G
AF059195 252229 MAFG
59 0.592 H010453_01 3-alpha hydroxysteroid
dehydrogenase type IIb
NM_016253 279801 LOC51708
60 0.685 H005634_01 Solute carrier family 11
(proton-coupled divalent metal ion transporters), member 3
NM_014585 5944 SLC11A3
61 0.68 H008745_01 Acid sphingomyelinase-like
phosphodiesterase
AK000184 42945 ASM3A
62 0.704 H003219_01 Glutathione S-transferase M3
(brain)
AF043105 2006 GSTM3
63 0.773 H003951_01 Predicted osteoblast protein D87120 29882 GS3786
64 0.735 H001047_01 Nidogen 2 AB009799 82733 NID2
65 0.792 H002382_01 Limbic system-associated membrane
protein
U41901 26479 LSAMP
66 0.623 H016583_01 1,2-alpha-mannosidase IC NM_020379 8910 HMIC
67 0.742 H011191_01 Lipin 2 D87436 166318 LPIN2
68 0.803 H002185_01 Niemann-Pick disease, type C1 AF002020 76918 NPC1
69 0.775 H000509_01 Neural precursor cell expressed,
developmentally down-regulated 4
D42055 1565 NEDD4
70 0.786 H007419_01 Progesterone membrane binding
protein
AJ002030 9071 PMBP
71 0.774 H002121_01 Paraoxonase 2 AF001601 169857 PON2
72 0.805 H008087_01 HSPC019 protein NM_014028 163724 HSPC019
73 0.696 H002393_01 Sema domain, immunoglobulin
domain (Ig), short basic domain, secreted, (semaphorin) 3C
AB000220 171921 SEMA3C
74 0.785 H014975_01 Homo sapiens mRNA; cDNA
DKFZp564N1272 (from clone DKFZp564N1272); complete CDS
AF087847 282654
75 0.614 H001215_01 Pentaxin-related gene, rapidly
induced by IL-1 beta
M31166 2050 PTX3
76 0.756 H002423_01 Vascular endothelial growth
factor B
U43368 78781 VEGFB
77 0.768 H010087_01 Destrin (actin depolymerizing
factor)
S65738 82306 ADF
78 0.742 H000025_01 Neutral sphingomyelinase
(N-SMase) activation associated factor
X96586 78687 NSMAF
79 0.744 H005560_01 WAS protein family, member 1 D87459 75850 WASF1
80 0.786 H014051_01 Very long-chain acyl-CoA
synthetase homolog 2
NM_012254 111401 VLCS-H2
81 0.644 H004741_01 Fibroblast growth factor 13 AF100143 6540 FGF13
82 0.764 H001605_01 Annexin A4 NM_001153 77840 ANXA4
83 0.71 H016019_01 Duodenal cytochrome b AL136693 31297 FLJ23462
84 0.804 H001346_01 Inositol(myo)-1(or
4)-monophosphatase 2
NM_014214 5753 IMPA2
85 0.635 H010918_01 WNT1 inducible signaling pathway
protein 2
AF100780 194679 WISP2
86 0.791 H001101_01 CD164 antigen, sialomucin D14043 43910 CD164
87 0.787 H004431_01 Rag C protein AF131773 110950 GTR2
88 0.792 H012626_01 Beta-2-microglobulin AB021288 75415 B2M
89 0.805 H002819_01 Protective protein for
beta-galactosidase (galactosialidosis)
AL008726 118126 PPGB
90 0.684 H002497_01 Complement component 1, r
subcomponent
M14058 1279 C1R
91 0.691 H006676_01 Lung type-I cell
membrane-associated glycoprotein
AF030428 135150 T1A-2
92 0.653 H012777_01 KIAA1199 protein AB033025 50081 KIAA1199
93 0.721 H003789_01 Colony stimulating factor 1
(macrophage)
M37435 173894 CSF1
94 0.849 H008439_01 SCO (cytochrome oxidase
deficient, yeast) homolog 1
AF026852 14511 SCO1
95 0.774 H008994_01 Solute carrier family 31 (copper
transporters), member 2
U83461 24030 SLC31A2
96 0.774 H010497_01 Interferon induced transmembrane
protein 3 (1-8U)
X57352 182241 IFITM3
97 0.762 H011175_01 Opsin 3 (encephalopsin) NM_014322 279926 OPN3
98 0.701 H011671_01 Short-chain
dehydrogenase/reductase 1
AF061741 17144 SDR1
99 0.767 H002804_01 Prion protein (p27-30)
(Creutzfeldt-Jakob disease, Gerstmann-Strausler-Scheinker syndrome,
fatal fami
U29185 74621 PRNP
100 0.792 H002258_01 UDP-glucose pyrophosphorylase 2 U27460 77837 UGP2
101 0.659 H001491_01 Cyclin T2 AF048731 155478 CCNT2
102 0.762 H002746_01 TNF receptor-associated factor 5 AB000509 29736 TRAF5
103 0.766 H013070_01 Sarcoglycan, epsilon AJ000534 110708 SGCE
104 0.761 H001062_01 N-acylsphingosine amidohydrolase
(acid ceramidase)
U70063 75811 ASAH
105 0.814 H002694_01 Glutathione peroxidase 4
(phospholipid hydroperoxidase)
X71973 2706 GPX4
106 0.774 H011917_01 Sorting nexin 3 AF034546 12102 SNX3
107 0.754 H006813_01 Homo sapiens cDNA FLJ11309 fis,
clone PLACE1010076
AK002171 28005
108 0.821 H002793_01 Antigen identified by monoclonal
antibodies 12E7, F21 and O13
M16279 177543 MIC2
109 0.844 H000474_01 Testis-specific kinase 1 D50863 79358 TESK1
110 0.731 H000930_01 Low density lipoprotein receptor
(familial hypercholesterolemia)
L00352 213289 LDLR
111 0.802 H009135_01 Electron-transferring-flavoprotein
dehydrogenase
S69232 323468 ETFDH
112 0.767 H008544_01 Atrophin-1 interacting protein 1;
activin receptor interacting protein 1
AB014605 22599 KIAA0705
113 0.789 H000400_01 Growth arrest-specific 6 L13720 78501 GAS6
114 0.762 H016469_01 MEK partner 1 NM_021970 6361 MP1
115 0.731 H002820_01 Ectodermal-neural cortex (with
BTB-like domain)
AF059611 104925 ENC1
116 0.75 H016592_01 Hypothetical protein FLJ12816 NM_022060 9175 FLJ12816
117 0.792 H006873_01 CGI-149 protein NM_016079 189658 LOC51652
118 0.592 H002066_01 Aldehyde dehydrogenase 1 family,
member A1
M31994 76392 ALDH1A1
119 0.689 H013490_01 H.sapiens polyA site DNA Z24724 4934
120 0.76 H015305_01 Hypothetical protein FLJ22029 NM_024949 285243 FLJ22029
121 0.704 H002566_01 Membrane metallo-endopeptidase
(neutral endopeptidase, enkephalinase, CALLA, CD10)
NM_007289 1298 MME
122 0.81 H002169_01 Sortilin-related receptor, L(DLR
class) A repeats-containing
NM_003105 278571 SORL1
123 0.88 H003649_01 Protein tyrosine phosphatase,
non-receptor type 6
X62055 63489 PTPN6
124 0.744 H011942_01 Activating transcription factor 5 AB021663 9754 ATF5
125 0.806 H007715_01 KIAA1091 protein AL117448 26797 KIAA1091
126 0.823 H012019_01 Epithelial protein lost in
neoplasm beta
NM_016357 10706 EPLIN
127 0.838 H010079_01 Hypothetical protein FLJ10337 AB037858 173484 KIAA1437
128 0.772 H003031_01 Glycoprotein A repetitions
predominant
Z24680 151641 GARP
129 0.762 H002785_01 Serine (or cysteine) proteinase
inhibitor, clade G (C1 inhibitor), member 1
X54486 151242 SERPING1
130 0.631 H000082_01 Deiodinase, iodothyronine, type II NM_013989 154424 DIO2
131 0.755 H007381_01 Hypothetical protein FLJ10044 AK000906 127273 FLJ10044
132 0.699 H014982_01 Tuftelin 1 NM_020127 283009 TUFT1
133 0.813 H003637_01 Protein tyrosine phosphatase,
non-receptor type 12
M93425 62 PTPN12
134 0.821 H002684_01 Bone morphogenetic protein 6 NM_001718 285671 BMP6
135 0.847 H001078_01 ATPase, Na+/K+ transporting, beta
3 polypeptide
NM_001679 76941 ATP1B3
136 0.785 H009413_01 KIAA0321 protein AB002319 8663 KIAA0321
137 0.806 H003439_01 Protein phosphatase 2 (formerly
2A), catalytic subunit, beta isoform
M60484 80350 PPP2CB
138 0.811 H011488_01 UDP-Gal:beta GlcNAc beta 1,4-
galactosyltransferase, polypeptide 5
AL035683 107526 B4GALT5
139 0.631 H002334_01 Cytochrome P450, subfamily I
(dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)
U03688 154654 CYP1B1
140 0.797 H006973_01 Homo sapiens cDNA FLJ10598 fis,
clone NT2RP2004841
AK001460 170873
141 0.737 H008497_01 Amyloid beta (A4) precursor-like
protein 2
NM_016160 279518 APLP2
142 0.802 H000517_01 Phorbol-12-myristate-13-acetate-induced
protein 1
D90070 96 PMAIP1
143 0.799 H007506_01 Clock (mouse) homolog AB002332 50722 CLOCK
144 0.831 H002305_01 Accessory proteins BAP31/BAP29 S74039 291904 DXS1357E
145 0.813 H002571_01 Meiotic recombination (S.
cerevisiae) 11 homolog B
AF022778 202379 MRE11B
146 0.795 H002782_01 Wee1+ (S. pombe) homolog X62048 75188 WEE1
147 0.814 H002076_01 Interleukin-1 receptor-associated
kinase 1
L76191 182018 IRAK1
148 0.82 H000048_01 PRKC, apoptosis, WT1, regulator U63809 176090 PAWR
149 0.578 H005801_01 Purkinje cell protein 4 U52969 80296 PCP4
150 0.834 H002311_01 Transcription factor 7-like 2
(T-cell specific, HMG-box)
Y11306 173638 TCF7L2
151 0.774 H008367_01 KIAA0623 gene product AB014523 151406 KIAA0623
152 0.809 H005443_01 Interferon-related developmental
regulator 1
AC005192 7879 IFRD1
153 0.796 H005941_01 Hypothetical protein FLJ20043 AK000050 103853 FLJ20043
154 0.731 H009185_01 KIAA1144 protein AB032970 22675 KIAA1144
155 0.737 H011708_01 Homo sapiens clone 24405 mRNA
sequence
AF070632 23729
156 0.848 H016365_01 Core1
UDP-galactose:N-acetylgalactosamine-alpha-R beta
1,3-galactosyltransferase
NM_020156 46744 C1GALT1
157 0.763 H010122_01 Homo sapiens mRNA; cDNA
DKFZp586F1223 (from clone DKFZp586F1223)
AL050204 28540
158 0.71 H002475_01 Pim-1 oncogene M54915 81170 PIM1
159 0.794 H007334_01 SH3 domain binding glutamic
acid-rich protein like
AF042081 14368 SH3BGRL
160 0.817 H000893_01 Major histocompatibility complex,
class I, E
X56841 181392 HLA-E
161 0.737 H010951_01 LIM domain only 4 NM_006769 3844 LMO4
162 0.846 H001759_01 Chloride channel 7 AL031600 80768 CLCN7
163 0.845 H001612_01 RAP1, GTP-GDP dissociation
stimulator 1
AF237413 7940 RAP1GDS1
164 0.753 H007858_01 Glutaminyl-peptide
cyclotransferase (glutaminyl cyclase)
X71125 79033 QPCT
165 0.808 H002897_01 Cathepsin L X12451 78056 CTSL
166 0.84 H004099_01 Phosphatidic acid phosphatase
type 2A
AF014403 41569 PPAP2A

SAM

‘Observed v. Expected’ table of GO classes and parent classes, in list of 166 genes shown above:

Only GO classes and parent classes with at least 5 observations in the selected subset and with an ‘Observed vs. Expected’ ratio of at least 2 are shown.

Cellular Component

GO id GO classification Observed in
selected subset
Expected in
selected subset
Observed/
Expected
0005887 integral to plasma membrane 19 9.37 2.03

Molecular Function

GO id GO classification Observed in
selected subset
Expected in
selected subset
Observed/
Expected
0016791 phosphoric monoester hydrolase activity 6 2.04 2.94
0005489 electron transporter activity 7 2.54 2.76
0042578 phosphoric ester hydrolase activity 6 2.4 2.5
0004713 protein-tyrosine kinase activity 5 2.16 2.31

Biological Process

GO id GO classification Observed in
selected subset
Expected in
selected subset
Observed/
Expected
0007600 sensory perception 6 1.92 3.13
0009581 detection of external stimulus 6 2.13 2.82
0006812 cation transport 6 2.93 2.05

SAM -ChromDist

View expression of significant genes.